Just finished a day each in Milford Sound and Doubtful Sound.
I did the sunriser classic with Roscos Kayak, a ~4 hours kayak through the Milford Sound area. Weather was excellent so it was very pleasant. We even saw a number of sea lions and penguins! I think the kayak is a good option compared to the short day cruise which I also went and was really disappointing. The day cruise was for 1.5-2 hours, and it’s not very interesting, waste of money.
I then did an overnight cruise at Doubtful Sound with Real Journeys which was great. Initially I thought it’s pricey, but after experiencing it myself I think it’s totally worth it, relative to say the Milford Sound day cruise. With the overnight cruise, you get to do short kayak, we sailed out to the Tasman Sea (sunset was good) and the dinner and breakfast buffet was excellent. Definitely worth the money spent! The crew and on-board service is fantastic! Also, Doubtful Sound is less popular because it’s harder to get to, you gotta go to Manapouri which is ~20mins drive from Te Anau, upon which you’ll board a ferry for an hour followed by an hour of bus to get to Ship Cove where you’ll board the cruise. The flip side is, there’s less ship there so it’s more peaceful.
In conclusion, I do think that at this time of the year, Milford looks more pretty given there’s still lots of snow-capped mountains around, while most snow are gone at Doubtful. However, Doubtful is multiple times bigger, so it’s more interesting for a longer overnight cruise. As with anything related to nature, it’s random so you need also to be lucky to have a good weather day!